13.08.21 | New lineages

New AY lineages

The latest release of the pangoLEARN model (2021-08-09) includes new lineages AY.4-AY.12. Many of these genome sequences may have previously been assigned to B.1.617.2 and these lineages are all subclades within B.1.617.2 that show significant geographic clustering: AY.4-AY.11 are predominantly found in the UK whereas AY.12 is a lineage detected predominantly in Israel. We’ve designated these as lineages to help researchers track the virus on a fine-scale (more on that below). These lineages remain the Delta variant, just as B.1.617.2 does, and their designation doesn’t imply any functional biological difference from B.1.617.2.

So why define new AY sub-lineages? The Delta variant has become widespread over the last number of months and B.1.617.2 is the predominant lineage in many countries worldwide. Classifying viral sequences as B.1.617.2 is useful to chart the rise of B.1.617.2 in a country, but once this lineage is dominant, it doesn’t allow researchers to easily do more fine-scale tracking. For example, in the UK currently, the majority of sequences are B.1.617.2 and, without doing more involved phylogenetic analyses, cases can only be linked at this very broad scale. The AY lineages break up B.1.617.2 into smaller related clusters that can be tracked separately. Each of these clusters is usually associated with a significant epidemiological event (for example, introduction into a new country with onward transmission) and will let researchers build a more fine-grained picture of how Delta variant is circulating nationally, and around the world.

We anticipate more AY lineages will follow soon. Unless stated otherwise by the WHO or other public health bodies, these lineages should be treated as the Delta variant and their designation to a sub-lineage doesn’t necessarily imply any functional biological difference from B.1.617.2.

Lineages are defined by a set of rules (outlined here). If you think you’ve identified a new lineage of B.1.617.2 based on these rules (or another lineage for that matter), please get in touch to let us know by submitting an issue here.



Pango lineages: guidelines for suggesting novel and recombinant lineages

13.04.22 | Christopher Ruis


Summary of designated Omicron lineages

01.04.22 | Christopher Ruis


Updates to Omicron lineage B.1.1.529

09.12.21 | Rachel Colquhoun